bids.variables.entities

Classes

Node(level, entities)	Base class for objects that represent a single object in the BIDS hierarchy.
NodeIndex()	Represents the top level in a BIDS hierarchy.
RunInfo(entities, duration, tr, image)	Attributes:
RunNode(entities, image_file, duration, …)	Represents a single Run in a BIDS project.

class Node(level, entities)

Base class for objects that represent a single object in the BIDS hierarchy.

Parameters:id (int, str) – A value uniquely identifying this node. Typically the entity value extracted from the filename via layout.

Methods

add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

Parameters:variable (BIDSVariable) – The Variable to add to the list.

class NodeIndex

Represents the top level in a BIDS hierarchy.

Methods

add_variable(variable)	Adds a BIDSVariable to the current Node’s list.
create_node(level, entities, *args, **kwargs)	Creates a new child Node.
get_collections(unit[, names, merge, …])	Retrieve variable data for a specified level in the Dataset.
get_nodes([level, entities, strict])	Retrieves all nodes that match the specified criteria.
get_or_create_node(level, entities, *args, …)	Retrieves a child Node based on the specified criteria, creating a new Node if necessary.

add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

Parameters:variable (BIDSVariable) – The Variable to add to the list.

create_node(level, entities, *args, **kwargs)

Creates a new child Node.

Parameters:

• level (str) – The level of analysis of the new Node.
• entities (dict) – Dictionary of entities belonging to Node
• kwargs (args,) – Optional positional or named arguments to pass onto class-specific initializers. These arguments are only used if a Node that matches the passed entities doesn’t already exist, and a new one must be created.

Returns:

A Node instance.

get_collections(unit, names=None, merge=False, sampling_rate=None, **entities)

Retrieve variable data for a specified level in the Dataset.

Parameters:

• unit (str) – The unit of analysis to return variables for. Must be one of ‘run’, ‘session’, ‘subject’, or ‘dataset’.
• names (list) – Optional list of variables names to return. If None, all available variables are returned.
• merge (bool) – If True, variables are merged across all observations of the current unit. E.g., if unit=’subject’ and return_type= ‘collection’, variablesfrom all subjects will be merged into a single collection. If False, each observation is handled separately, and the result is returned as a list.
• sampling_rate (int, str) – If unit=’run’, the sampling rate to pass onto the returned BIDSRunVariableCollection.
• entities – Optional constraints used to limit what gets returned.

Returns:

A list of BIDSVariableCollections if merge=False; a single BIDSVariableCollection if merge=True.

get_nodes(level=None, entities=None, strict=False)

Retrieves all nodes that match the specified criteria.

Parameters:

• level (str) – The level of analysis of nodes to return.
• entities (dict) – Entities to filter on. All nodes must have matching values on all defined keys to be included.
• strict (bool) – If True, an exception will be raised if the entities dict contains any keys that aren’t contained in the current index.

Returns:

A list of Node instances.

get_or_create_node(level, entities, *args, **kwargs)

Retrieves a child Node based on the specified criteria, creating a new Node if necessary.

Parameters:

• level (str) – The level of analysis of the Node.
• entities (dict) – Dictionary of entities to include in newly-created Nodes or filter existing ones.
• kwargs (args,) – Optional positional or named arguments to pass onto class-specific initializers. These arguments are only used if a Node that matches the passed entities doesn’t already exist, and a new one must be created.

Returns:

A Node instance.

class RunInfo(entities, duration, tr, image)

Attributes:

duration

Alias for field number 1

entities

Alias for field number 0

image

Alias for field number 3

tr

Alias for field number 2

Methods

count($self, value, /)	Return number of occurrences of value.
index($self, value[, start, stop])	Return first index of value.

count($self, value, /)

Return number of occurrences of value.

duration

Alias for field number 1

entities

Alias for field number 0

image

Alias for field number 3

index($self, value, start=0, stop=sys.maxsize, /)

Return first index of value.

Raises ValueError if the value is not present.

tr

Alias for field number 2

class RunNode(entities, image_file, duration, repetition_time)

Represents a single Run in a BIDS project.

Parameters:

• id (int) – The index of the run.
• entities (dict) – Dictionary of entities for this Node.
• image_file (str) – The full path to the corresponding nifti image.
• duration (float) – Duration of the run, in seconds.
• repetition_time (float) – TR for the run.
• task (str) – The task name for this run.

Methods

add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

get_info

add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

Parameters:variable (BIDSVariable) – The Variable to add to the list.